Using the bio3d package.
library(bio3d)
pdb <- read.pdb("1hel")
## Note: Accessing on-line PDB file
pdb
##
## Call: read.pdb(file = "1hel")
##
## Total Models#: 1
## Total Atoms#: 1186, XYZs#: 3558 Chains#: 1 (values: A)
##
## Protein Atoms#: 1001 (residues/Calpha atoms#: 129)
## Nucleic acid Atoms#: 0 (residues/phosphate atoms#: 0)
##
## Non-protein/nucleic Atoms#: 185 (residues: 185)
## Non-protein/nucleic resid values: [ HOH (185) ]
##
## Protein sequence:
## KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
## RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
## QAWIRGCRL
##
## + attr: atom, xyz, seqres, helix, sheet,
## calpha, remark, call
Let’s use a bioinformatics method called NMA (Normal Mode Analysis) to predict the dynamics (flexibility) of this enzyme.
modes <- nma(pdb)
## Building Hessian... Done in 0.055 seconds.
## Diagonalizing Hessian... Done in 0.204 seconds.
plot(modes)
Make a “move” of its predicted motion. We often call this a “trajectory”.
mktrj(modes, file="nma.pdb")